Pokemon After Effects
by Trentopia
Summary: Welcome to the world of pokemon, Crow an aspire pokemon researcher is thrown into the frey on his 18th birthday when he is told to go to Mr. Pokemon's house to pick up a package for Professor Elm. Set five years after the events of the fourth generation remakes of Pokemon gold and silver. I don't own pokemon, just the story. Rated t just to be safe Probably could be rated e
1. prologue

_Welcome to the world of Pokemon, My name is Samuel Oak, I am a pokemon professor. In my travels around the world I have studied many pokemon and fostered the growth of many young trainers. Many people study pokemon, some battle with pokemon as their partners, other simply enjoy living side by side with pokemon as friends._

 _There are some in this world who would use pokemon for evil. These people have taken many names, Rocket, Magma, Aqua, Galactic, and these organizations have all been wiped out by trainers who shared deep bonds with their pokemon. Trainers have fought to save this world from the darkness that the evil teams foster, and only by a hair have they been able to win against these evil forces. The Dex Holders are a team of powerful trainers, who guard their region from these dark forces, and with their bonds with their pokemon, prevail against the forces of darkness._

 _Gold, Silver, Red, Blue, Pearl, Diamond, Platinum, Ruby, Emerald, Sapphire, White, and Black are a few of these powerful trainers, the Dex Holders. Your Journey starts in Johto, where Gold and Silver have not been seen for months and the dark force of Nexus Rocket is on the rise in a final bid for power that will leave Johto broken._

Crow, an eighteen year old boy, his dirty blond hair was cut short on the sides and left a bit longer on the top, and his green eyes glistened in the morning sun. His partner pokemon a Cyndaquil, accompanied him everywhere, not always in a pokeball, but sometimes. Crow wore a blue jacket with a black tee shirt under it, with black denim pants, his go to outfit for everything.

Crow's hometown of Pallet was a fading memory. Four years ago he had moved to New Bark Town with his mom, and Crow had become the assistant to Professor Elm, a man who was often lost in his own little world. Most days Crow would stroll along in the woods close to New Bark Town, and gaze at the many pokemon, taking notes and drawing sketches for the professor. Crow would pack away his things and head back to the lab to give the professor his research. The boy would also be sent to the neighboring towns to collect items from some of Elm's acquaintances, or to buy supplies from the nearest pokemart. Crow studied, on his own, the geological effects of pokemon, and how the evolutionary stones helped pokemon to evolve. Crow admired Professor Elm who had helped him on the road to becoming a pokemon professor. Elm gave Crow an allowance of ten thousand pokedollars a year to further his research, and with this money Crow was almost able to buy his own lab. Crow barreled used the money Elm gave him, only for essential things for research.

Dawn arose one early monday morning and Crow got out of bed, putting on a blue jacket with a tall collar, Crow grabbed his pokemon, a cyndaquil named Thunder, then made his way to Elm's lab. The lab was accompanied with white tile, and only one window, to let very little natural light in, The ac always ran a little strong so even in the warm months a jacket would be needed inside the lab. Sitting at his desk in the lab, Crow booted up his laptop, and was greeted to a barrage of emails from Elm, Oak, and other professors and some friends, all of which said "Happy eighteenth birthday!" Elm walked in and sat a plate of cupcakes, that his wife had made, down on the table where all the assistants ate lunch.

"Crow, Happy birthday!" Elm cheered. "Now a man huh?"

"Yes, sir," Crow answered in his respectful tone of voice.

"Good, well I hate to do this to you on your birthday, but could you run a fast errand for me?" Elm asked.

"Anything Professor," Crow didn't mind working on his birthday, and thought it would be good to get out of the lab just a little.

"PERFECT!" Elm cheered happily. "I need you to go to Mr. Pokemon's house and pick up a couple items for me from the Pokemart. A few pokeballs, and a piece of mail."

Yes sir!" Crow stood up and shut his laptop. The boy walked out the door and made his way to Cherrygrove City. Cherrygrove City was booming with personality and life. The City was full of color and held a lively tone of music coming from the pokemon center. The blue roofed Pokemart stood next to the center, and Crow made his way inside to buy the pokeballs and mail that Elm had requested. The clerk behind the counter greeted Crow with a smile and asked what he could help with, and Crow gave him the list of what he needed. The transaction was short and Crow was able to stop by the pokemon center quickly to heal Thunder, before making his way north to Mr. Pokemon. Crow was in a bit of a hurry, as he was excited to tell Professor Elm of his plan to build a research center in Cherrygrove City.

Route 30 wasn't very long and was full of pokemon, Crow was almost ashamed that he didn't bring a sketchpad to draw some of the scenery here. The warm mid morning air made the hike fun and relaxing and less like a chore for Crow. Ledyba buzzed overhead and sentrets scurried in between the trees. In the distance sat Mr. Pokemon's house, able to observe it all the time, a twinge of jealousy stung Crow, as he wished for a view like this every day. Crow walked up to the door of the house and knocked three time.

An old man answered the door, inviting Crow to come inside. It had been almost two months since Crow had visited the house, but not much had changed since then. Mr Pokemon's house was warm and cozy, having little in the way of lab equipment, one wouldn't be able to even tell that Mr. Pokemon was a pokemon researcher once. The old man had a large belly and gruff beard now, but the kind heartedness was still in his eyes and smile. The man welcomed Crow in with a smile and wished him a happy birthday.

"Now, I don't do this much," Mr. Pokemon said in a happy tone, "But I am too old now to raise any pokemon. I have an eevee, and some evolutionary stones, and Elm and I decided that since you were going into the field of pokemon research then it would be a very appropriate gift to give you these stone and pokemon." Mr. Pokemon broke into a short coughing fit after finishing his sentence. "I'm fine. I'm fine." The old man said as Crow rushed to support him. "I'm just getting past a nasty cold."

Crow walked to the sink and filled a glass of water for the old man who graciously accepted. Mr. Pokemon handed Crow the pokemon and items and the two talked for a few minutes. "So when are you going to take your journey?" Mr. Pokemon asked.

"I really wasn't planning on one, actually." Crow sighed. "I'm not much for battling, and I would much rather stay and help the professor."

"Don't be silly boy," Mr. Pokemon laughed. "How do you plan to be a Professor if you have never been on a journey with your pokemon? Stats are all well and good, but there is a bond you can only be found by forging it in battle."

"I see," Crow knew that Mr. Pokemon was telling the truth, but he didn't want to leave Elm alone just to go battle pokemon.

"Even old man Oak was a famous trainer before becoming a professor," Mr. Pokemon took a sip of the water trying to suppress a cough, but it failed and the old man fell into another fit.

"I don't know," Crow continued, "like I said, i'm not a very good battler."

"No one is when they first start off, do you think Blue was always the famous battler he is now? What about Red?"

"So I should go on an adventure then," Crow wasn't asking more like confirming it for himself. "I've never even been to Violet City before."

"Then go!" The old man laughed. "Go and explore the world while you're young."

"I'll have to see if Elm is okay with it first, he is my boss after all." Crow sighed.

"Well before you go, I have one more gift for you, a pokedex. It will record information on pokemon you catch automatically, this could be useful for someone wanting to be a professor, No?" The pokedex was small and no bigger than the size of a smartphone. Crow put it in his pocket next to his Pokegear.

"Thank you," Crow bowed as he made his way to the wooden door. Crow left the house and made his way back to Cherrygrove City. As Crow walked south he thought about what Mr. Pokemon had said, still unsure about what he wanted to do. Crow made the excuse of not being a good battler, but he wasn't actually that bad, and it wouldn't hurt to explore the region and catch new pokemon, but Crow didn't really want to leave where he felt comfortable. Crow sent out his new eevee and petted it, the boy knew that Mr. Pokemon had given eevee to him because of its unique ties to the evolutionary stones, and because it was a good pokemon in general, good to go on an adventure.

The small cat-fox pokemon made a purring noise as Crow petted it, the soft fur ruffling beneath the boy's fingers. The eevee soon sat on his shoulder as Crow walked towards New Bark Town. The eevee was light and Crow decided to give it the nickname of Milo.. After a couple of wild battles, Milow and Crow finally made it home and walked back to the lab where Elm sat in the rolling chair facing the door, a grin stapled across his face. "Good afternoon, Crow, I see you like mine and Mr. Pokemon's gift?"

"Yes, professor." Crow admitted, about to bring up his plans for a new lab and for an adventure.

"Good, now, I need you to go to Goldenrod City for me, it will be about a month trek, but I need you to find professor Oak, and give him that letter, but first let me write what I need to." Elm swiped the letter away, and started to vigorously write what he needed to. "Now, Crow, bring this letter to Oak, on your way, you will probably want to challenge the pokemon gyms, the badges will come in handy when using the H.M.s."

"Okay," was all Crow could stammer, he had just got back, with big news and was being sent away again. Sure he was happy he was going to get to go on the adventure, but he wanted to at least tell Elm of his plan to open a research center in Cherrygrove City, but didn't because he didn't want to distract from his current errand, nor start Elm on how important staying focused was.

"Now Falkner is the first gym leader, an electric type pokemon will do well against him, or a rock type, with his pokemon being flying and all." Elm shooed Crow out of the door and left the boy to run his errand.

Crow sighed and made his way home to tell his mom of the trek he would be going on. She cheered with joy and wished him luck. With the sun just now ringing noon, Crow made his way back to Cherrygrove.

On his way Crow saw a young boy being attacked by a Noctowl. Crow rushed to the boys aid, sending out Thunder. Thunder charged the large bird distracting it long enough for the boy to escape towards Cherrygrove City. Crow was now locked into a fight against a much stronger opponent than he would be able to fight. The noctowl sent a barrage of tackles, all of which Thunder dodged and countered with ember and tackle. Noctowl didn't seem too affected by Thunder's attacks, Thunder tried to power up using its blaze ability, but this was still not enough to start to overpower the large bird. The bird slammed into the small pokemon and sent it flying. In the air Thunder sent another barrage of embers, all of which hit home in the Noctowl's eye. The now blinded bird flurried around and was left open for Thunder to continue the attacks.

A large lightning bolt from behind Crow made the boy turn around to see the little boy he had saved standing with a larger man with a dark tan and long brown hair. A large ampharos stood behind the two, and fired off another thunder to keep the bird down. "Boy," the man yelled at Crow, "get outa here and take my boy with you, you did good, but now its my turn to battle this bird."

Crow did what he was told and got the little boy to safety in Cherrygrove city. A while later the Man walked into the pokemon center to see Crow and the little boy waiting for him. The man nodded at Crow and walked up to the counter to heal his pokemon. While waiting the man turned to Crow and said, "Thank you for saving my boy, I captured the noctowl to keep it from hurting anyone else. What's your name?"  
"Crow, sir," Crow answered quickly. "Nice to meet you Crow, the name is Sampson, and that's my boy Oli, short fer Oliver."

Sampson invited Crow to his house and they sat and had tea. "Why was the noctowl attacking Oli?" Crow asked.

"I don't know, but lately some pokemon have been acting strange, ya know? More aggressive, I have captured a few of these and have managed to rehabilitate them, but I am not too sure as to what has caused this, I don't think it is a disease, but I am not smart about this kinda stuff."

"I hope I never run into one that strong again." Crow half laughed about it.

"If you do give me a call, Ill come and help, it is the least I can do."


	2. Ch 1: Falkner's Choice, the Tower

Two days have passed since our hero left on his journey across the Johto region to find Professor Oak in Goldenrod city. After defeating a rogue noctowl, Crow stayed the night with his new friend Sampson, the father of a young boy named Oli. Now our hero marches onward into the famous Violet city, to take on Gym Leader Falkner.

The Team so far.

Thunder, Cyndaquil, lvl 12

Milo, Eevee, Lvl 9

"Thunder, use Ember!" Crow shouted at the top of his lungs, the pokemon did as requested and sent flaming coals at an opposing caterpie. The bug pokemon squealed as the attack struck. Crow ordered for a tackle to follow, then the caterpie was unable to battle, and Crow had won the match. "You put up a good fight," Crow said to his opponent, a young bug catcher around the age of twelve, "keep training hard and aim for the top." Crow accepted his prize money and headed away from the battle grounds, his next stop the pokemon center in Violet City. The city had a vibrant hue of red that lumbered over the entire town, giving it a mystic and old feel. A large tower loomed and swayed to the north of the town, but Crow's goal was the gym.

Crow walked into the pokemon center and let his pokemon heal. After a short while Crow left the center and made his way through the city, experiencing all there was to see and taking it all vibrant music that hung in the air, reminded Crow of when he was a kid playing video games in his room in Pallet Town. The beautiful aroma of flowers and dark wood filled his nose. Crow pondered for a moment about trying to open his research center here, if it would be at all possible, but then he thought about the other towns and cities he would go to, and maybe he would like them even more.

Crow walked around the town eventually finding the gym. The large building had a man blocking the entrance. The man was just taller than Crow, but he was incredibly scrawny. His hair was platinum in color, and dropped into his face. "Good morning, lad," the man said as he saw Crow approach him. "I'm guessing you want to battle Falker, am I right?"

"Yes, sir." Crow answered trying to get around the man and into the building, failing.

"Well it seems you are going to have to wait," the man bowed apologetically. "It seems Falkner isn't accepting visitors at the moment, kicked me out rather quickly he did."

"You're a trainer?" Crow said taking notice that the man looked rather old.

"More like a scientist, I have business with the gym leader, but the idiot doesn't seem to want my help," the old man's tone hinted at there being a problem. "You see, lad, the Sprout Tower, the tall building i'm sure you saw when you came to town, is said to be haunted and I wanted Falkner's permission to examine the tower, him being the gym leader and all kinda makes him sorta in charge of the City and what goes on in it. I didn't want to do something that would interfere with his wishes."

The haunted tower sparked Crows interest, "why do you say haunted?"

"OOooooh those are just rumors, but if a strong enough ghost pokemon was in there it could be dangerous to the people training in the tower… Ah!"

"What's the 'Ah!' for?" Crow asked scared.

"While I am not a battler to be sure, you look like someone who could handle getting into a bit of harmless mischief," the man explained. "If you wanted, you could go to the tower and find this powerful ghost pokemon and if there is one, then you could take it out, either in a battle, or even capturing it. I wouldn't need Falker to help me, nor his permission as anyone is allowed in the tower to train, right?"

"I'm not too sure about this," Crow replied.

"But, lad, you will be protecting all those in the tower who are unaware of the ghost pokemon, and even gain a powerful ally by doing so. Win win for you I say. All I would need you to do afterwards is return to me and tell me about the experience and I will surely compensate you." The old man laughed and continued talking. "My name, by the way is Dr. Gyro, I study pokemon behavior in abnormal circumstances, and this will greatly further my research if we could find such a powerful ghost type pokemon laying in wait in the tower. You and me, we will be famous. OH I can hear it now. Dr. Gyro and.. Er what is your name again?"

"Crow, my name is Crow."

"Wonderful!" the doctor exclaimed. "Dr. Gyro and Crow the saviors of Sprout Tower!"

"I'll help you, but don't tie me into this when you publish your paper on ghost pokemon." Crow sighed, realizing that since Falkner wasn't going to let him into battle right now, then he might as well help the crazy scientist with his research to pass the time.

Perfect. I can't wait, I will be waiting at the base of the tower for your return, I cannot tell you how grateful I am for your help lad!" Crow went on without Gyro, and made his way up to the tower. The tall building swayed in the wind and Crow popped his head in to see that the training hub was empty of everyone but a single man. The old man was bald and wore a dark purple robe.

"Good afternoon boy," the man spoke softly. "My name is Sage Harold, welcome to sprout tower. We haven't had many visitors lately, they have all been scared off by the ghost."

"Can you tell me about the ghost?" Crow asked as he approached the man.

"It is an odd pokemon, normally the ghost pokemon only come out at night, but this one is different. I believe it is a Haunter, though the ghastly here don't normally evolve, because of all the low level pokemon here they don't get enough experience fighting to evolve."

"Why would a haunter want to cause havoc in the tower?" Crow asked then followed up with "what floor is it normally on?"

"I don't know why, but normally it is seen on the third floor." Sage Harold said. "If you are going after it, I wish you luck."

Crow walked up the stairs to the second floor where the wooden boards creaked under his feet with every step. Crow was forced to battle the Sages in the tower to make sure his pokemon were trained well enough to continue up. The battles were quick as all the sages had low level bell sprouts, so Thunder was able to sweep them away with a couple of embers.

Crow passed through a pair of doors and was greeted by the wicked smile of a haunter trying to scare him away, it almost worked to as it made Crow fall back out of shock. The twisted laugh of the pokemon told Crow that it was like the noctowl he had faced the other day, rouge. The boy stood back up and wiped off his pants. Crow chased the ghost pokemon up the stairs through to the third floor, the haunters domain. At the third floor he was forced into a battle with the twisted ghost pokemon, Thunder came out of its pokeball and sent embers flying at the ghost as it did. Crow dialed up Sampson and told him what was going on and where he was, asking for help. Thunder jumped and dodged out of the way of the opposing pokemon's attacks. Slowly the small fire pokemon was able to whittle down the Hp of the haunter. Soon the haunter had enough of the game and started to get serious in the fight. The ghost send a barrage of shadow balls flying towards Thunder. Just as the move was about to hit the cyndaquil Milo jumped out and blocked the ghost type move, nullifying the effects. "It's not a fair fight like this, but I don't have a choice, I guess," Crow mumbled to himself as he thought of a strategy for his pokemon. Eevee took up a defensive spot where he could jump in front of a ghost attack to nullify it, while Thunder sent out ember after ember at the ghost.

"This is it, come on!" Crow cheered as his pokemon battled. "Go pokeball!" Crow sent a pokeball flying towards the hunter, who was ensnared into its red beam of light. The pokeball twitched three times then sent out a small ding sounding a successful capture. Crow picked up the ball, his first captured pokemon, a rouge haunter. Rouge. Crow nicknamed the haunter Rouge, symbolizing the pokemon's past. "Let's go boys." Crow sighed. Crow checked the Hp of his pokemon showing that they all could use a trip to the pokemon center. On his way back out of the tower, Sampson was coming up and they bumped heads.

"Where is it? The haunter?"

"Right here," Crow held up his newest pokemon showing Sampson the spoils of his victory.

"You caught it?" A shocked expression crossed the man's face.

"It wasn't easy. Both Milo and Thunder had to fight it at once."

"That strong huh?" Sampson calmed down and walked Crow out of the tower and they ran into Dr. Gyro at the bottom of it.

"Sooo?" The doctor asked. "Did you get it?"

"I did," Crow sighed.

"And? What did you learn from it?"

"It was a rouge pokemon, forced to evolve too early its only a level fifteen." Sampson said. "I checked on my dex."

"So it is possible then. This confirms so many of my theories, thank you both sooo much!" The doctor cheered. "And like I said," Gyro handed Crow a nugget, "I'll be sure to compensate you." With that Gyro left and headed into the direction of Cherrygrove city.

"I don't like him." Sampson said as he followed Crow to the pokemon center. "Too odd,"

"I know what you mean," Crow answered.

"Why were you helping him?" Sampson asked.

"I wasn't really, I wanted to keep the tower a safe place for trainers to train, not help a crazy man." Crow laughed at that, "our goals just correlined, plus he is the one who told me about the rouge haunter."

"I see, well you should've called me before going into battle with it, you could've been hurt bad." Sampson scolded Crow but continued, "but good job on winning, it looks like you won't be needing my help with rogues like I thought you would." Sampson let out a quiet laugh. "I'll be seeing you around." Sampson walked towards Cherrygrove, following the Doctor who he was still suspicious of.

Crow walked into the pokemon center and let the nurse take his pokemon for a few minutes. When he got them back he decided to see if Falkner would battle him. Crow walked to the tall gym building and made his way inside to see Falkner standing in the center of the gym. His hair was long and a light hue of purple, and his clothes resembled that of a karate instructor, save that his were green. "My name is Falkner, and what might I call you?"

"My name is Crow, Im here for a battle."

"Well people say you can clip a bird pokemons wings with electricity, but Ill prove them wrong. Meet me at the top of the tower when you are ready for our match." Falkner turned and walked up to an elevating platform to go up to the top, when he got off the platform moved back to ground level where Crow could get on to go up. When crow stood on the platform the whining of the gears started and Crow slowly moved upwards. The top level was a glass floor full of scrapes and dents, and didn't look very safe, but Crow continued towards Falkner.

"I know that you helped the doctor," Falkner started. "I didn't want to interfere with anything in the tower, as people tend to not like to visit the gym for a while whenever they see me leave the tower, I guess they think I go to train. So thank you for helping me, in a way, but that doesn't mean I'll go easy on you."

"I understand, and I wouldn't have it anyother way."

"Good, this will be a one on one match, I hope you brought an electric type pokemon with you, you'll need it."Falkner sent out a pidgeotto, and Crow sent out Thunder. "A fire type then, I expected something better, oh well. Pidgeotto, wing attack!"

"Thunder, dodge it, then use ember."

"No good, now pidgeotto, gust, blow those away!"

"Thunder smokescreen."

"Dang, Pidgeotto, try to blow the smoke away."

"Smokescreen fill the room!"

"No! Pidgeotto, Peck before you can't see him!"

"Ember now!"

"Critical? No, we can't lose pidgeotto, peck again."

"Haha Miss, again ember, then follow it with a tackle!"

"I concede. You win Crow." Falkner admitted his defeat as his pokemon was unable to battle. "It was a cheap trick lowering my accuracy like that, but a good strategy nonetheless"

"Thank you!" Crow bowed in appreciation and stood back up.

"Keep training hard, you have potential kid, one of these days you'll maybe even beat the elite four. Here is your badge you earned it." Falkner handed Crow the shiney chrome badge, the Zephyr badge.

Crow left the gym and returned to the pokemon center to stay the night before heading south towards Azalea Town the next morning.


End file.
